I think science fiction is now a dead genre because people won't accept it as a good, fun experience unless it abides absolutely by the scientific literature.

Take it for what it is: a fun story with good gameplay and great humor. I don't think the game is meant to be super-duper realistic.

Before Starwars arrived sci-fi was scientific in the sense everything needed to be logical and have a grounded framework in reality. Then Starwars basically made it part fantasy/adventure without the startrek or early 60/70's sci-fi movies like need to explain everything. That's basically the realm Portal 2 is in. It has a talking Potatoes for Christ sake.

The bigger plot hole is how the final chamber is so close to the surface, yet she had to go through another whole mile to get to the top.

Plus I don't think GLaDOS put chell in a Biome, she doesn't need her anymore, and she doesn't want to keep her restricted because she knows that Chell would just keep on escaping anyway. PLUS it appears that she is at the surface at a parking lot near Aperture Science, yet the lift takes her to a field in the middle of nowhere...

Okay, she probably is in a biome now.

I think we are taking this game too seriously, there are a tonne of plot holes in this game that don't fit the first portal, it's there to be enjoyed, and Valve did a damn good job I'd say.